March 3, 2017

A new map to help understand plant gene function and evolution

A paper published in Science today (29th July 2011), presents the first large-scale protein network map for a plant species. It is hoped that the map will help efforts to functionally characterise unknown proteins which account for 60% of all genes in Arabidopsis. Such characterisation is important to explain the molecular basis for phenotypic variation in plants, especially where this information can be used to inform marker assisted plant breeding programmes.

In common with similar studies, the network resulting from binary interactions of 8000 Arabidopsis proteins is of the highly-interconnected "small world" type, typified by a small number of 'hub' nodes with a high number of connections, and also a number of sub-network 'cliques'. Such patterns are being used to investigate the functions of connected proteins.

Of particular interest to plant biology, where duplicated genes (paralogs) are common due to relatively frequent genome duplication events and high transposon activity, is the distribution of such gene pairs within the map. Neofunctionalisation, where redundant genes take on a new function post-duplication, causes characteristic patterns of disruption to the network which abate over time as the network stabilises.

Eagle Genomics are proud to be associated with this ground-breaking work from the Arabidopsis Interactome Mapping Consortium. In particular Eagle Director William Spooner, working with the Gramene project at Cold Spring Harbor Laboratory, contributed data on Arabidopsis paralogues generated by the Ensembl Compara Gene Tree method.

Topics: Big data technology, Bioinformatics